1XME

Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb1XME/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus
Expression System: Thermus thermophilus HB8
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2004-10-01 Released: 2005-03-22
Deposition Author(s): Hunsicker-Wang, L.M., Pacoma, R.L., Chen, Y., Fee, J.A., Stout, C.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.217
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 87.88 kDa
Atom Count: 6,177
Modelled Residue Count: 756
Deposited Residue Count: 770
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide I	A	568	Thermus thermophilus	Mutation(s): 0 Gene Names: cbaA EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for Q5SJ79 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ79 Go to UniProtKB: Q5SJ79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SJ79
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide II	B	168	Thermus thermophilus	Mutation(s): 0 Gene Names: cbaB, ctaC EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for Q5SJ80 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ80 Go to UniProtKB: Q5SJ80
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SJ80
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide IIA	C	34	Thermus thermophilus	Mutation(s): 0 Gene Names: cbaD EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P82543 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P82543 Go to UniProtKB: P82543
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P82543
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HAS Query on HAS Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	HEME-AS C₅₄ H₆₄ Fe N₄ O₆ PDYODZVCODUKFH-ZOMLSHGTSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
BNG Query on BNG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.217
R-Value Observed: 0.217
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.902	α = 90
b = 114.902	β = 90
c = 177.064	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-03-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-03-22
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary

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1XME

Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)